Highly Reviewed and Tested Templates

These templates cover the main analytics steps and allow continuous improvement and integration.

Multi-Omics Data Insights

Type of Analysis Skills and Tools
Gene expression analysis RNA-seq, STAR, DESeq, Snakemake, R, Python
Workflow
Gene enrichment analysis RNA-seq, STAR, DESeq, Snakemake, R, Python
Workflow
Variant calling analysis BWA, Snakemake,
Workflow
Genome wide association study kGWASflow,
Workflow
Single Cell Analysis scRNASeq, Scanpy, Python, Jupyter Notebook
Workflow
Amplicon data analysis (16S) Mothur, QIIME2, R, Python
Workflow: In progress
Metagenomics data analysis
Microbial and pathway profiling		 Biobakery, R, Python
Workflow: In progress
Microbiome Machine learning models MikropML, Caret, Snakemake, R, Python
Workflow
Gene Ontology Enrichment GO, Proteomics, Snakemake, R, Python
Workflow




Machine learning models

Model Tools
Logistic Regression MikropML, Caret, Snakemake, R, Python
Workflow: In progress
Rainfall forest Snakemake, R, Python
Workflow: In progress
Support vector machine Snakemake, R, Python
Workflow: In progress




Quantitative Data Analysis

Analysis Tools
Precipitation & drought Snakemake, R, Python
Workflow: In progress
Temperature anomalies Snakemake, R, Python
Workflow: In progress
Time Series Analysis R, Python
Workflow: In progress

Goal: Sustainable Data Analysis

  • Reproducibility
  • Adaptability
  • Transparency

Reference: https://f1000research.com/articles/10-33

Aspects to consider for sustainable data analysis.

Example of Snakemake workflow syntax

A

B



Differentially Expressed Genes




Gene Set GO-Based Enrichment




Gene user-Set Enrichment




Variant calling








Genome wide association study




Gene Ontology Enrichment




Single Cell Analysis




Number of genes

Highly variable genes

Principal Component analysis

Biomarker Discovery




Microbial profiling




Machine learning models




Quantitative data analysis

Daily global drought index (Standardized z-scores for ~50years).





Temperature anomalies from 1880 (inner layer) to present (2022, outer layer).

Helpfull Ideas